Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for PCYT1B
Basic gene info.Gene symbolPCYT1B
Gene namephosphate cytidylyltransferase 1, choline, beta
SynonymsCCTB|CTB
CytomapUCSC genome browser: Xp22.11
Genomic locationchrX :24576203-24665455
Type of geneprotein-coding
RefGenesNM_001163264.1,
NM_001163265.1,NM_004845.4,
Ensembl idENSG00000102230
DescriptionCCT BCCT-betaCT BCTP:phosphocholine cytidylyltransferase bcholine-phosphate cytidylyltransferase Bphosphorylcholine transferase B
Modification date20141207
dbXrefs MIM : 604926
HGNC : HGNC
Ensembl : ENSG00000102230
HPRD : 05376
Vega : OTTHUMG00000021270
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PCYT1B
BioGPS: 9468
Gene Expression Atlas: ENSG00000102230
The Human Protein Atlas: ENSG00000102230
PathwayNCI Pathway Interaction Database: PCYT1B
KEGG: PCYT1B
REACTOME: PCYT1B
ConsensusPathDB
Pathway Commons: PCYT1B
MetabolismMetaCyc: PCYT1B
HUMANCyc: PCYT1B
RegulationEnsembl's Regulation: ENSG00000102230
miRBase: chrX :24,576,203-24,665,455
TargetScan: NM_001163264
cisRED: ENSG00000102230
ContextiHOP: PCYT1B
cancer metabolism search in PubMed: PCYT1B
UCL Cancer Institute: PCYT1B
Assigned class in ccmGDBC

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Phenotypic Information for PCYT1B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PCYT1B
Familial Cancer Database: PCYT1B
* This gene is included in those cancer gene databases.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PCYT1B
MedGen: PCYT1B (Human Medical Genetics with Condition)
ClinVar: PCYT1B
PhenotypeMGI: PCYT1B (International Mouse Phenotyping Consortium)
PhenomicDB: PCYT1B

Mutations for PCYT1B
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PCYT1B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI952718PCYT1B13287X2466819024676354GALNT1281404183327097533271098
AI656193PCYT1B13287X2466819024676354GALNT1281404183327097533271098

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=39)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr23:24597510-24597510p.R211C3
chr23:24608151-24608151p.E159K2
chr23:24625952-24625952p.D82N2
chr23:24608208-24608208p.R140C2
chr23:24608226-24608226p.E134K2
chr23:24608140-24608140p.K162N1
chr23:24665167-24665167p.S19F1
chr23:24580418-24580418p.E368Q1
chr23:24608229-24608229p.Y133N1
chr23:24593350-24593350p.N265S1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 3171   2  63   53 4
# mutation 3161   2  63   53 5
nonsynonymous SNV 3151   2  42   42 4
synonymous SNV   1       21   11 1
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chrX:24608140p.K144N,PCYT1B2
chrX:24608229p.E350G,PCYT1B1
chrX:24580417p.E141K,PCYT1B1
chrX:24690710p.R14C1
chrX:24597473p.E350Q,PCYT1B1
chrX:24608231p.F139S,PCYT1B1
chrX:24580418p.G3G1
chrX:24690741p.S321L,PCYT1B1
chrX:24597530p.L135L,PCYT1B1
chrX:24608251p.S317L,PCYT1B1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for PCYT1B in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for PCYT1B

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

AIPL1,BCL2L14,BYSL,CCDC67,E2F3,ETV6,GPM6B,
GPR161,JAKMIP2,NR2E1,P2RX3,PAQR9,PCYT1B,SOHLH2,
tAKR,TAS1R1,TET1,TTLL8,UCHL1,USP49,ZNF705D
ARHGAP19,CACNA1C,COL17A1,COL4A5,COL4A6,GRIA4,ITGA2,
NEO1,NFASC,PCYT1B,PTPRT,RARB,SDK2,SEMA5A,
SEPT3,SHC4,SLC27A6,SRGAP3,SV2A,ZNF561,ZNF648

ATP1B2,BAI3,C14orf132,CEND1,CNTN2,DCAF12L2,GPR88,
GRIA1,HMP19,KCNK3,MLLT11,NACAD,PCYT1B,PDZD4,
RGAG4,RND2,SALL2,SLC22A17,TAGLN3,TCEAL5,TMEFF2
ACTG2,ACTN1,AOC3,ATP1A2,BVES,CALD1,CNN1,
CTXN1,DACT3,FAM46B,FLNA,RBFOX3,ITGB3,NLGN1,
PCYT1B,PDLIM7,PYGM,SGCD,SLC8A2,TAGLN,ZFHX4
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for PCYT1B
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00122phosphate cytidylyltransferase 1, choline, betaapproved; nutraceuticalCholine


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Cross referenced IDs for PCYT1B
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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